I do not want this to be a chassis vs. PU debate. It is already established that Renault and Honda had the least amount of peak power in relation to Ferrari and Mercedes. Strictly in IMO, the MP4-31 had rear suspension issues in its basic design. This in turn had an effect on everything else. I have heard and read about how good or bad the chassis was and so on, or that McLaren was always running a low DF set up compared to the others. I will say that if you compare the Mercedes customer cars, that should give some indication on how much a difference the chassis alone can make. I am not a suspension or aero efficiency expert but I really believe that chassis development is just as if not more labor intensive and time consuming to achieve significant improvements that the PU.
This year getting tire temperatures and mechanical grip to desired levels proved extremely difficult and much higher levels of DF were run than anticipated to get the rear to work. This in turn required more than anticipated adjustments to the front to offset increased under steer. Many think that is was good that numerous FW changes were made from race to race to show how aggressive and progressive the chassis manufacturer but sometimes the opposite is true; like a dog chasing its own tail. I don't know of any F1 driver that prefers under-steer to a slight over-steer condition if given the two choices. I think the public did hear both Button and Alonso complain throughout the season of under steering issues. I believe this stems from the rear suspension issue. At times it was frustrating to me to hear how good the chassis was in comparison to the others. It was also "interesting" to me to hear that McLaren was always running low DF compared to others. That definitely was not the case. Again IMO, aero efficiency was an issue this season. It is established that Honda had the lowest ICE output of the four, but that was not the sole reason for lower speed trap readings.
If you can make the opposition flinch, you have already won.